28 Indian J. Fish., 61(2) : 28-34, 2014 Introduction Grouper species are usually identified by their colour pattern as well as meristic characters including pyloric caecae counts (Heemstra and Randall, 1993). Molecular techniques are used as a powerful method to confirm species and also to bring out the evolutionary history. RAPD (Random Amplified Polymorphic DNA) analysis is a technique based on polymerase chain reaction (PCR) amplification of discrete regions of the genome with short oligonucleotide primers of arbitrary sequence (Welsh and McClelland, 1990; Williams et al., 1990). This method is simple and quick to perform and most importantly, no prior knowledge of the genetic make-up of the organism in question is required (Hadrys et al., 1992). It requires only minute amounts of template DNA with which the complete genome is screened. Genetic polymorphisms can be visualised within 24h from the extraction of genomic DNA. The storage of this genetic material is also easy. RAPD technique has some limitations like limited reproducibility across laboratories, dominance of markers and limited applicability above generic level for systematic studies. Among DNA fingerprinting techniques, it requires the least in technology, labour and expenditure (Caetano-Anolles et al., 1991; Hadrys et al., 1992; Black, 1993). Resolution of taxonomic ambiguity in groupers (Pisces: Serranidae) by the random amplified polymorphic DNA (RAPD) technique T. S. C. ROY 1 , A. GOPALAKRISHNAN 2 , P. M. A. MUNEER 3 , L. JOHN 3 , K. K. MUSAMMILU 3 AND V. S. BASHEER 3 1 Society of Integrated Coastal Management (SICOM-MoEF), #9, Institutional Area, Lodhi Road New Delhi - 110 003, India 2 Central Marine Fisheries Research Institute, Kochi - 682 018, Kerala, India 3 National Bureau of Fish Genetic Resources (NBFGR) Cochin Unit, CMFRI Campus, P. B. No. 1603 Kochi - 682 018, Kerala, India e-mail: dr.tcroy@gmail.com ABSTRACT In this study, a species specific molecular marker RAPD (Random Amplified Polymorphic DNA) was used for resolving taxonomic ambiguity in groupers thereby helping in species identification. Fishes were collected from the coast of Mandapam and Keelakkarai, Tamil Nadu. RAPD patterns were developed for 8 species of groupers and each one had a unique RAPD profile. The phylogenetic relationships of these species were also analysed. Keywords: Grouper, Phylogeny, RAPD, Taxonomic ambiguity RAPD technique has been proven to be a valuable technique for species identification and confirmation in fishes (Dinesh et al., 1993; 1995; Bardakci and Skibinski, 1994; Naish et al., 1995; Bielawski and Pumo, 1997; Elo et al., 1997; Callejas and Ochando, 1998; Liu et al., 1998; Williams et al., 1998). It can also be used to confirm species identity in groupers (Parenrengi, 2001; Ansenio et al., 2002; Upadhyay et al., 2006; Saad et al., 2012) especially in captive breeding where the stocking of broodstocks based on their morphological appearance has to be supported with other identification techniques to ensure precise pairing (Bakar and Azizah, 2000). Materials and methods Collection of specimens Freshly caught specimens of eight species of groupers were obtained from fishing boats off the coast of Mandapam and Keelakkarai (9 0 13’ N - 9 0 18’ N and 78 0 50’ E - 79 0 10’ E) along the south-eastern coast of Tamil Nadu. The fishes were photographed either in the fishing boats or as soon as they were brought to the landing centres. The species were initially sorted into different groups as per their colour pattern and then identified to the species level based on the morphological and meristic characters especially the pyloric caecae counts (Roy, 2004).